diff --git a/doc/manual_references.bib b/doc/manual_references.bib index a681381a1..06f44481e 100644 --- a/doc/manual_references.bib +++ b/doc/manual_references.bib @@ -1747,6 +1747,16 @@ @Article{parekh:2004 doi = {10.1029/2003GB002061} } +@Article{parekh:2005, + author = {Parekh, P. and Follows, M. J. and Boyle, E. A.}, + title = {Decoupling of iron and phosphate in the global ocean}, + journal = {Global Biogeochemical Cycles}, + year = {2005}, + volume = {19}, + pages = {}, + doi = {10.1029/2004GB002280} +} + @Article{parkinson:79, author = {Parkinson, C. L. and W. M. Washington}, title = {A Large-Scale Numerical Model of Sea Ice}, @@ -1866,6 +1876,16 @@ @Article{ringeisen:20 doi = {10.5194/tc-2020-153} } +@Article{rios:1998, + author = {Ríos, A. F. and Fraga, F. and Pérez, F. F. and Figueiras, F. G.}, + title = {Chemical composition of phytoplankton and {Particulate} {Organic} {Matter} in the {Ría} de {Vigo} ({NW} {Spain})}, + journal = {Sciencia Marina}, + volume = {6 2}, + number = {3}, + year = {1998}, + pages = {257--271}, +} + @Article{roach:15, author = {Roach, C. J. and H. E. Phillips and N. L. Bindoff and S. R. Rintoul}, year = 2015, diff --git a/doc/phys_pkgs/darwin.rst b/doc/phys_pkgs/darwin.rst index 91aaea60b..beb38e7ea 100644 --- a/doc/phys_pkgs/darwin.rst +++ b/doc/phys_pkgs/darwin.rst @@ -362,13 +362,15 @@ General parameters are set in namelist :varlink:`DARWIN_PARAMS`: :varlink:`uptakeTempAe` & 0.0 & 1/K & temperature coefficient for uptake (TEMP_VERSION 4) :varlink:`alpfe` & 0.04 & & solubility of Fe dust :varlink:`scav` & 0.4/year & 1/s & fixed iron scavenging rate + :varlink:`scav_tau` & 0.2 & & factor for converting Th scavenging rates to iron ones + :varlink:`scav_inter` & 0.079 / day & L\ :sup:`e` mg\ :sup:`-e` s\ :sup:`-1` & intercept of scavenging power law (e=e\ :sub:`scav`) + :varlink:`scav_exp` & 0.58 & & exponent of scavenging power law + :varlink:`scav_POC_wgt` & 0.02173 & g/mmol |nbsp| C & weight POC contributes to POM + :varlink:`scav_POSi_wgt` & 0.069 & g/mmol |nbsp| Si & weight POSi contributes to POM + :varlink:`scav_PIC_wgt` & 0.100 & g/mmol |nbsp| C & weight PIC contributes to POM :varlink:`ligand_tot` & 1D-3 & mol/m\ :sup:`3` & total ligand concentration :varlink:`ligand_stab` & 2D5 & m\ :sup:`3`/mol & ligand stability rate ratio :varlink:`freefemax` & 0.4D-3 & mol/m\ :sup:`3` & max concentration of free iron - :varlink:`scav_rat` & 0.005 / day & 1/s & rate of POM-based iron scavenging - :varlink:`scav_inter` & 0.079 & & intercept of scavenging power law - :varlink:`scav_exp` & 0.58 & & exponent of scavenging power law - :varlink:`scav_R_POPPOC` & 1.1321D-4 & mmol P / mmol C & POP\:POC ratio for :varlink:`DARWIN_PART_SCAV_POP` :varlink:`depthfesed` & -1.0 & m & depth above which to add sediment source (was -1000) :varlink:`fesedflux` & 1D-3 / day & mmol Fe /m\ :sup:`2`/s & fixed iron flux from sediment :varlink:`fesedflux_pcm` & 0.68D-3 & mmol Fe / mmol C & iron input per POC sinking into bottom for :varlink:`DARWIN_IRON_SED_SOURCE_VARIABLE` diff --git a/doc/phys_pkgs/darwin_iron.rst b/doc/phys_pkgs/darwin_iron.rst index 50db37794..2683dd4d4 100644 --- a/doc/phys_pkgs/darwin_iron.rst +++ b/doc/phys_pkgs/darwin_iron.rst @@ -88,21 +88,42 @@ The scavenging rate for free iron is .. math:: r_{{\text{scav}}}= \begin{cases} - r_{{\text{scav}}}I_{{\text{scav}}}\op{POC}^{e_{{\text{scav}}}} - & \text{for POM-based scavenging,} \\ \op{scav} - & \text{for constant scavenging.} + & \text{for fixed-rate scavenging,} \\ + \tau_{{\text{scav}}}I_{{\text{scav}}}\op{POM}^{e_{{\text{scav}}}} + & \text{for particle-based scavenging.} \end{cases} -To select POM-based scavenging, #define :varlink:`DARWIN_PART_SCAV`. -If :varlink:`DARWIN_PART_SCAV_POP` is defined, :math:`\op{POC}` is -replaced by :math:`\op{POP}\!/R^{\op{POP}:\op{POC}}_{{\text{scav}}}`. +To select particle-based scavenging following Parekh et al. (2005) +:cite:`parekh:2005`, define :varlink:`DARWIN_PART_SCAV`. POM is the +concentration of particulate organic matter in units of mg/L. It is +parameterized in terms of POC, POSi and PIC, -The concentration of free iron is determined following -Parekh et al. (2004) :cite:`parekh:2004` and -Dutkiewicz et al. (2005) :cite:`dutkiewicz:2005`. Free dissolved iron, -Fe', is assumed to be in equilibrium with dissolved iron bound -to ligands, FeL, +.. math:: + + \op{POM} = w^{\text{scav}}_{\text{POC}} \op{POC} + + w^{\text{scav}}_{\text{POSi}} \op{POSi} + + w^{\text{scav}}_{\text{PIC}} \op{PIC} + \;. + +The value for :math:`w^{\text{scav}}_{\text{POC}}` is taken from Rios et al. +(1998) :cite:`rios:1998` as the weight of as detritus without opal per mol of +carbon. :math:`w^{\text{scav}}_{\text{POSi}}` and +:math:`w^{\text{scav}}_{\text{PIC}}` are just the molecular weights of opal +(per mol Si) and calcium carbonate, see +:numref:`tab_phys_pkgs_darwin_iron_params`. + +The old (and deprecated) formulation of scavenging in terms of POP can be +recovered by defining :varlink:`DARWIN_PART_SCAV_POP`, in which case +:math:`\op{POM}` is replaced by +:math:`\op{POP}\!/R^{\op{POP}:\op{POC}}_{{\text{scav}}}`. Parameter names and +defaults are different in this case, see +:numref:`tab_phys_pkgs_darwin_scav_pop`. + +The concentration of free iron, Fe', is determined following Parekh et al. +(2004) :cite:`parekh:2004` and Dutkiewicz et al. (2005) +:cite:`dutkiewicz:2005`. Free dissolved iron is assumed to be in equilibrium +with dissolved iron bound to ligands, FeL, .. math:: \op{Fe}' + L' \rightleftharpoons \op{FeL} @@ -133,6 +154,7 @@ and after each biogeochemical subtimestep. :delim: & :widths: auto :header: Parameter, Symbol, Default, Units, Description + :name: tab_phys_pkgs_darwin_iron_params :varlink:`alpfe` & :math:`\alpha_{\op{Fe}}` & 0.04 & & solubility of Fe dust :varlink:`depthfesed` & :math:`d_{\op{sed}}` & -1.0 & m & depth above which to add sediment source @@ -144,10 +166,24 @@ and after each biogeochemical subtimestep. :varlink:`solFeVent` & :math:`\alpha_{\op{Fe}}^{\op{vents}}` & 0.002 & & solubility of iron from hydrothermal vents :varlink:`R_FeHe3_vent` & :math:`R^{\op{Fe:^3He}}_{\op{vents}}` & 4.5E8 & mol Fe / mol :sup:`3`\ He & Fe:\ :sup:`3`\ He ratio for hydrothermal vents :varlink:`scav` & scav & 0.4/year & 1/s & fixed iron scavenging rate - :varlink:`scav_rat` & :math:`r_{\op{scav}}` & 0.005 / day & 1/s & rate of POM-based iron scavenging - :varlink:`scav_inter` & :math:`I_{\op{scav}}` & 0.079 & & intercept of scavenging power law + :varlink:`scav_tau` & :math:`\tau_{\op{scav}}` & 0.2 & & factor for converting Th scavenging rates to iron ones + :varlink:`scav_inter` & :math:`I_{\op{scav}}` & 0.079 / day & L\ :sup:`e` mg\ :sup:`-e` s\ :sup:`-1` & intercept of scavenging power law (e=e\ :sub:`scav`) :varlink:`scav_exp` & :math:`e_{\op{scav}}` & 0.58 & & exponent of scavenging power law - :varlink:`scav_R_POPPOC` & :math:`R^{\op{POP:POC}}_{\op{scav}}` & 1.1321E-4 & mmol P / mmol C & POP\:POC ratio for :varlink:`DARWIN_PART_SCAV_POP` + :varlink:`scav_POC_wgt` & :math:`w^{\op{scav}}_{\op{POC}}` & 0.02173 & g/mmol |nbsp| C & weight POC contributes to POM + :varlink:`scav_POSi_wgt` & :math:`w^{\op{scav}}_{\op{POSi}}` & 0.069 & g/mmol |nbsp| Si & weight POSi contributes to POM + :varlink:`scav_PIC_wgt` & :math:`w^{\op{scav}}_{\op{PIC}}` & 0.100 & g/mmol |nbsp| C & weight PIC contributes to POM :varlink:`ligand_tot` & :math:`L_{\op{T}}` & 1E-3 & mmol/m\ :sup:`3` & total ligand concentration - :varlink:`ligand_stab` & :math:`\beta_{\op{stab}}` & .2E6 & m\ :sup:`3`/mmol & ligand stability rate ratio + :varlink:`ligand_stab` & :math:`\beta_{\op{stab}}` & 0.2E6 & m\ :sup:`3`/mmol & ligand stability rate ratio :varlink:`freefemax` & :math:`\op{Fe}'_{\op{max}}` & 0.4E-3 & mmol/m\ :sup:`3` & max concentration of free iron + + +.. csv-table:: Iron parameters for :varlink:`DARWIN_PART_SCAV_POP` + :delim: & + :widths: auto + :header: Parameter, Symbol, Default, Units, Description + :name: tab_phys_pkgs_darwin_scav_pop + + :varlink:`scav_rat` & :math:`\tau_{\op{scav}}` & 0.005 / day & 1/s & rate factor + :varlink:`scav_inter` & :math:`I_{\op{scav}}` & 0.079 & L\ :sup:`e` mg\ :sup:`-e` & intercept of scavenging power law (e=e\ :sub:`scav`) + :varlink:`scav_exp` & :math:`e_{\op{scav}}` & 0.58 & & exponent of scavenging power law + :varlink:`scav_R_POPPOC` & :math:`R^{\op{POP:POC}}_{\op{scav}}` & 1.1321E-4 & mmol |nbsp| P / g & POP\:POC ratio